Package Bio :: Package SeqIO :: Module PhylipIO
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Module PhylipIO

source code

Bio.SeqIO support for the "phylip" (PHYLIP) file format.

You were expected to use this module via the Bio.SeqIO functions. This module has now been replaced by Bio.AlignIO.PhylipIO, and is deprecated.

Classes [hide private]
  PhylipWriter
Write interlaced Phylip sequence alignments.
Functions [hide private]
 
PhylipIterator(handle, alphabet=SingleLetterAlphabet())
Reads a Phylip alignment file returning a SeqRecord object iterator.
source code
Variables [hide private]
  __warningregistry__ = {('Bio.SeqIO.PhylipIO is deprecated. Yo...
Function Details [hide private]

PhylipIterator(handle, alphabet=SingleLetterAlphabet())

source code 

Reads a Phylip alignment file returning a SeqRecord object iterator.

Record identifiers are limited to at most 10 characters.

It only copes with interlaced phylip files! Sequential files won't work where the sequences are split over multiple lines.

For more information on the file format, please see: http://evolution.genetics.washington.edu/phylip/doc/sequence.html http://evolution.genetics.washington.edu/phylip/doc/main.html#inputfiles


Variables Details [hide private]

__warningregistry__

Value:
{('Bio.SeqIO.PhylipIO is deprecated.  You can continue to read and wri\
te \'clustal\' files with Bio.SeqIO, but this is now handled via Bio.A\
lignIO internally.',
  <type 'exceptions.DeprecationWarning'>,
  17): 1}